Re: [OpenBabel-scripting] [openbabel-scripting] Open Babel Warnings

[A. S. <oli...@ya...>]

Chris Morley wrote:
> 
> A. Sebastian wrote:
>> I use OpenBabel Perl Module to parse mol files to a database and by the
>> way I
>> use the following code to obtain smiles format:
>> 	my $obMol=new Chemistry::OpenBabel::OBMol;
>> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
>> 	$obConversion->SetInAndOutFormats("mol","smi");
>> 	$obConversion->ReadString($obMol,$mol_file);
>> 	my $outSmiles=$obConversion->WriteString($obMol);
>> 
>> All works OK, but I obtain sometimes warning messages on screen that make
>> slower the process, I'd like to avoid this messages but I don't know how
>> to
>> do that.
>> 
>> An example of the warning messages:
>> *** Open Babel Warning  in WriteMolecule
>>   1-[(4-Acetyl-phenylcarbamoyl)-methyl]-pyridinium Proton(s)
>> added/removed
>> 
>> With the InChi format I have success avoiding this messages with this
>> code:
>> 	my $obMol=new Chemistry::OpenBabel::OBMol;
>> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
>> 	$obConversion->SetInAndOutFormats("mol","inchi");
>> 	$obConversion->ReadString($obMol,$mol_file);
>> 	$obConversion->SetOptions("w",1);
>> 	my $outInchi=$obConversion->WriteString($obMol);
>> 
>> I want to know if exists a similar solution for smiles, because the
>> former
>> doen't work ($obConversion->SetOptions("w",1);)
>> 
> 
> You can control the severity of OpenBabel error messages that are 
> displayed in C++ code using:
> 
> obErrorLog.SetOutputLevel(0);
> 
> 0 supresses all the messages; 5 allows everything.
> 
> OpenBabel::obErrorLog is a global variable; the number is an enum of 
> type obMessageLevel. I don't know how well this works in the Perl 
> version, but if it doesn't we should do something about it.
> 
> obErrorLog.StopLogging();
> is an alternative to supress everything.
> 
> (In the command-line version use the option ---errorlevel n )
> 
> Chris
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 

Finally I tried adding the following perl lines:

	my $obMessageHandler=new Chemistry::OpenBabel::OBMessageHandler;
	$obMessageHandler->StopLogging();

And I obtained the following error:

Can't locate Chemistry/OpenBabel/OBMessageHandler.pm in @INC (@INC contains:
/etc/perl /usr/local/lib/perl/5.8.7 /usr/local/share/perl/5.8.7
/usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
/usr/local/lib/site_perl .)

Perhaps there is something wrong in the former two lines of my code, or
could be the problem that the class OBMessageHandler is not implemented in
Perl?

Alvaro
-- 
View this message in context: http://www.nabble.com/Open-Babel-Warnings-tf2080646.html#a5874719
Sent from the openbabel-scripting forum at Nabble.com.